title: Asymmetric processing of a substrate protein in sequential allosteric cycles of AAA+ nanomachines.
abstract: Essential protein quality control includes mechanisms of substrate protein (SP) unfolding and translocation performed by powerful ring-shaped AAA+ (ATPases associated with various cellular activities) nanomachines. These SP remodeling actions are effected by mechanical forces imparted by AAA+ loops that protrude into the central channel. Sequential intra-ring allosteric motions, which underlie repetitive SP-loop interactions, have been proposed to comprise clockwise (CW), counterclockwise (CCW), or random (R) conformational transitions of individual AAA+ subunits. To probe the effect of these allosteric mechanisms on unfoldase and translocase functions, we perform Langevin dynamics simulations of a coarse-grained model of an all-alpha SP processed by the single-ring ClpY ATPase or by the double-ring p97 ATPase. We find that, in all three allosteric mechanisms, the SP undergoes conformational transitions along a common set of pathways, which reveals that the active work provided by the ClpY machine involves single loop-SP interactions. Nevertheless, the rates and yields of SP unfolding and translocation are controlled by mechanism-dependent loop-SP binding events, as illustrated by faster timescales of SP processing in CW allostery compared with CCW and R allostery. The distinct efficacy of allosteric mechanisms is due to the asymmetric collaboration of adjacent subunits, which involves CW-biased structural motions of AAA+ loops and results in CW-compatible torque applied onto the SP. Additional simulations of mutant ClpY rings, which render a subset of subunits catalytically-defective or reduce their SP binding affinity, reveal that subunit-based conformational transitions play the major role in SP remodeling. Based on these results we predict that the minimally functional AAA+ ring includes three active subunits, only two of which are adjacent.
authors.affiliation: Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio 45221, USA.
authors.forename: Andrea N
authors.initials: AN
authors.lastname: Kravats
authors.forename: Sam
authors.initials: S
authors.lastname: Tonddast-Navaei
authors.forename: Ryan J
authors.initials: RJ
authors.lastname: Bucher
authors.forename: George
authors.initials: G
authors.lastname: Stan
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000494:Allosteric Regulation; D056004:Molecular Dynamics Simulation; D036103:Nanotechnology; D011487:Protein Conformation; D058767:Protein Unfolding; D013379:Substrate Specificity
chemical_list: D000251:Adenosine Triphosphatases